rnaQUAST Installation from the Release Archive - weaponsforge/fastractor GitHub Wiki

rnaquast notes

The following notes installs rnaQUAST from the GitHub release archive on an Ubuntu 18.0.4.2 machine using pyenv.

WARNING!

The following steps produces an erroneous rnaQUAST installation. All dependencies doesn't look to installed after installing the required python packages using pip, nor the ones described in requirements.txt. There are errors reported on running the rnaQUAST.py --test command.

It is highly recommended to install rnaQUAST using conda with virtual environments. All dependencies (and their proper versions) are automatically installed, and rnaQUAST.py --test runs without errors. Read on the tutorial rnaQUAST Installation Using Conda(https://github.com/weaponsforge/fastractor/wiki/rnaQUAST-Installation-Using-Conda) for more information on installing rnaQUAST using conda.

Content

Requirements

The following requirements and dependencies were used for this project. Other system and software configurations are open for testing.

  1. Virtual Box 6.14 (for Windows OS)
  2. Ubuntu 18.04.2
  3. pyenv (pyenv-installer)
    • this tool will be used to install and manage various Python versions
    • Python 3.6 will be used for the rnaQUAST installation, but other Python versions will also be used for other projects
  4. Python
    • installed using pyenv
    • version 3.6
    • pip
  5. BLAST
  6. GMAP

Install the Python Dependencies

  1. Install pyenv.

    • Install pyenv's build dependencies. 
      sudo apt-get install -y build-essential libssl-dev zlib1g-dev libbz2-dev \
libreadline-dev libsqlite3-dev wget curl llvm libncurses5-dev libncursesw5-dev \
xz-utils tk-dev libffi-dev liblzma-dev python-openssl git
    • Follow the instructions resulting from #2 on how to add pyenv to the systemt path variable. For example, add the ff. on top topmost lines of the ~/.bashrc file and save (nano ~/.bashrc): 
      # Load pyenv automatically by adding
# the following to ~/.bashrc:
export PATH="/home/adminuser/.pyenv/bin:$PATH"
eval "$(pyenv init -)"
eval "$(pyenv virtualenv-init -)"
    • Source out the .bashrc file.
      source ~/.bashrc
    • Restart your machine.

  2. Install Python 3.6 using pyenv.

    • view the list of available Python3.* versions.
      pyenv install --list | grep " 3\.[678]"
    • Install the target Python version 3.6.0. 
      pyenv install -v 3.6.0
pyenv rehash
    • Verify the installed Python versions from pyenv.
      pyenv versions

Install the External Software Dependencies

  1. Install BLAST
    • Download NCBI BLAST+ (blastn) link(https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/) (version 2.11.0+-1)
      wget https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.11.0+-x64-linux.tar.gz
    • Extract blast from the archive.
      tar -zxvf ncbi-blast-2.11.0+-x64-linux.tar.gz
    • Install blast on your system.
      • Go to the /bin directory.
        cd bin
      • export the bin path to the system PATH variable 
        cat <<EOF | sudo tee /etc/profile.d/blast.sh
export PATH=$PATH:/YOUR_EXTRACTED_BLAST_BIN_PATH
EOF
      • Source out the created blast.sh.
        source /etc/profile.d/blast.sh
      • Verify the blast installation.
        blastn -version
  2. Install GMAP link(http://research-pub.gene.com/gmap/) (BLAT is also an alternate option)
    • Download the GMAP tar archive.
      wget http://research-pub.gene.com/gmap/src/gmap-gsnap-2021-02-12.tar.gz
    • Extract the archive.
      tar -zxvf gmap-gsnap-2021-02-12.tar.gz
    • Install gmap. 
      cd gmap-gsnap-2021-02-12
./configure
make
make check   (optional)
sudo make install
    • Verify the gmap installation.
      gmap -version

rnaQUAST Installation

  1. Download the latest rnaQUAST release. Version 2.2.0 is the latest version as of this writing.
    wget -O rnaquast-v2.2.0.tar.gz https://github.com/ablab/rnaquast/archive/v2.2.0.tar.gz
  2. Extract rnaquast from the archive.
    tar -zxvf v2.2.0.tar.gz
  3. Use Python version 3.6.0 for the rnaquast project. 
    cd rnaquast-v2.2.0
pyenv local 3.6.0
  4. Install rnaquast's python dependencies. 
    pip install matplotlib
pip install joblib
pip install biopython // biopython is required from gffutils below
pip install gffutils
  5. Verify your installation.
    python rnaQUAST.py --test
  6. To run rnaQUAST on your data use the following command: 
    python rnaQUAST.py \
--transcripts /PATH/TO/transcripts1.fasta /PATH/TO/ANOTHER/transcripts2.fasta /PATH/TO/MULTIPLE/*.fasta [...] \
--reference /PATH/TO/reference_genome.fasta --gtf /PATH/TO/gene_coordinates.gtf